Computational insights into structural and optical properties of P-containing and N-containing ligands capped CdSe clusters

ABSTRACT

The ligand effects on the structures and properties (energetics, binding energies, charge distribution and optical properties) of the (CdSe)_n clusters (n?=?3, 6, and 10) with P-containing (PH₃, PH₂Me, PHMe₂ and PMe₃) and N-containing (NH₃, NH₂Me, NHMe₂ and NMe₃) have been studied using density functional theory. The P atom and N atom in the ligands interact with Cd and form Cd–P and Cd–N bonds. The influence of P-containing ligands can be enhanced with increasing CH₃ of ligands, while the N-containing ligands influence slightly change. A blueshift in absorption band was predicted for the clusters with increasing CH₃ of P-containing ligands. We also found that the calculated binding energies for various ligands are found to decrease in the order PMe₃?>?NH₂Me?>?NHMe₂?>?NH₃?>?NMe₃?>?PHMe₂?>?PH₂Me?>?PH₃. The use of hydrogen atom for modelling of the CdSe cluster passivating ligands is found to yield unphysical results as well.     

Structures and electronic properties of CumConO2(m + n = 2–7) clusters

A theoretical study was carried out of Cu_mCo_nO₂(2?≤?m?+?n?≤?7) clusters using density functional method. O₂ molecules are adsorbed at top sites. After adsorption, O₂ molecules are activated. The Δ₂ E value of CuCo₃O₂ cluster is obviously the smallest, indicating that its thermodynamic stability is the worst. While Cu₆CoO₂ displays stronger chemical stability. Charge transfer from Cu–Co to anti-bonding orbital of O₂, which leads to O–O getting longer. The Mulliken charge population and PDOS analysis are also discussed.     

Probing the structural and electronic properties of aluminum-sulfur Al n S m (2 ≤ n + m ≤ 6) clusters and their oxides

Using the first-principle density functional calculations, the equilibrium geometries and electronic properties of anionic and neutral aluminum-sulfur Al _n S _m (2?≤?n?+?m?≤?6) clusters have been systematically investigated at B3PW91 level. The optimized results indicate that the lowest-energy structures of the anionic and neutral Al _n S _m clusters prefer the low spin multiplicities (singlet or doublet) except the Al₂￣, Al₂, S₂, Al₄ and Al₂S₄ clusters. A significant odd-even oscillation of the highest occupied-lowest unoccupied molecular orbital (HOMO-LUMO) energy gaps for the Al _n S _m ￣ clusters is observed. Electron detachment energies (both vertical and adiabatic) are discussed and compared with the photoelectron spectra observations. Furthermore, a good agreement between experimental and theoretical results gives confidence in the most stable clusters considered in the present study and validates the chosen computational method. In addition, the variation trend of chemical hardness is in keeping with that of HOMO-LUMO energy gaps for the Al _n S _m clusters. Upon the interaction of oxygen with the stable AlS _m ￣ clusters, the dissociative chemisorptions are favorable in energy. The binding energy and Gibbs free energy change show completely opposite oscillating behaviors as the cluster size increases.     

Effects of smoking severity and moderate and severe periodontitis on serum C-reactive protein levels: an age- and gender-matched retrospective cohort study

Abstract

Background and purpose: C-reactive protein (CRP) which might affect cardiovascular events can be affected by chronic diseases and smoking. Since the effects of smoking dosage as well as the mutual effect of smoking and periodontitis on CRP levels have not been evaluated, we aimed to assess these.

Materials and methods: This retrospective age- and gender-matched study was performed on 120 dental patients. Clinical attachment loss, pocket probing depth (PPD), bleeding on probing (BoP), O’Leary plaque index and serum CRP were recorded. Patients were divided into one control and five cohort groups (n?=?20 each) according to smoking severity [pack years (PY) below or above 30] and periodontal condition (healthy periodontium and moderate/severe periodontitis). The effects of clinical measurements, age, gender, smoking and periodontitis on CRP were assessed using one- and two-way analyses of variance, Tukey and Bonferroni post hoc tests, and multiple linear regression (α?=?0.05).

Results: CRP concentrations were 0.07255?±?0.009539, 0.09645?±?0.010625, 0.122235?±?0.018442, 0.3758?±?0.187369, 0.81595?±?0.0410299 and 1.8717?±?0.652728?mg/l, respectively, in the control (PY?≤?30 with healthy periodontium), cohort 1 (PY?>?30 with healthy periodontium), cohort 2 (PY?≤?30 with moderate periodontitis), cohort 3 (PY?>?30 with moderate periodontitis), cohort 4 (PY?≤?30 with severe periodontitis) and cohort 5 (PY?>?30 with severe periodontitis). The positive effects of age, smoking severity, periodontitis and PPD, on CRP increase were significant (Regression p?<?0.02). BoP had a negative effect (p?=?0.015).

Conclusions: Clinicians should warn the patients, especially the older ones, about the effects of their gingival health and smoking on their cardiovascular condition.     

All-electron scalar relativistic calculation of water molecule adsorption onto small gold clusters

An all-electron scalar relativistic calculation was performed on Au _n H₂O (n = 1–13) clusters using density functional theory (DFT) with the generalized gradient approximation at PW91 level. The calculation results reveal that, after adsorption, the small gold cluster would like to bond with oxygen and the H₂O molecule prefers to occupy the single fold coordination site. Reflecting the strong scalar relativistic effect, Au _n geometries are distorted slightly but still maintain a planar structure. The Au–Au bond is strengthened and the H–O bond is weakened, as manifested by the shortening of the Au–Au bond-length and the lengthening of the H–O bond-length. The H–O–H bond angle becomes slightly larger. The enhancement of reactivity of the H₂O molecule is obvious. The Au–O bond-lengths, adsorption energies, VIPs, HLGs, HOMO (LUMO) energy levels, charge transfers and the highest vibrational frequencies of the Au–O mode for Au _n H₂O clusters exhibit an obvious odd-even oscillation. The most favorable adsorption between small gold clusters and the H₂O molecule takes place when the H₂O molecule is adsorbed onto an even-numbered Au _n cluster and becomes an Au _n H₂O cluster with an even number of valence electrons. The odd–even alteration of magnetic moments is observed in Au _n H₂O clusters and may serve as material with a tunable code capacity of “0” and “1” by adsorbing a H₂O molecule onto an odd or even-numbered small gold cluster.     

A systematic search for the structures,stabilities, and electronic properties of bimetallic Ca<Subscript>2</Subscript>-doped gold clusters: comparison with pure gold clusters

The local meta-GGA exchange correlation density functional (TPSS) with a relativistic effective core potential was employed to systematically investigate the geometric structures, stabilities, and electronic properties of bimetallic Ca₂Au _n (n = 1–9) and pure gold Au _n (n ≤ 11) clusters. The optimized geometries show that the most stable isomers for Ca₂Au _n clusters have 3D structure when n > 2, and that one Au atom capping the Ca₂Au _n−1 structure for different-sized Ca₂Au _n (n = 1–9) clusters is the dominant growth pattern. The average atomic binding energies and second-order difference in energies show that the Ca₂Au₄ isomer is the most stable among the Ca₂Au _n clusters. The same pronounced even–odd alternations are found in the HOMO–LUMO gaps, VIPs, and hardnesses. The polarizabilities of the Ca₂Au _n clusters show an obvious local minimum at n = 4. Moreover, the inverse corrections to the polarizabilities versus the ionization potential and hardness were found for the gold clusters.     

Density functional theory study of small nickel clusters

The stable geometries and atomization energies for the clusters Ni _n (n = 2–5) are predicted with all-electron density functional theory (DFT), using the BMK hybrid functional and a Gaussian basis set. Possible isomers and several spin states of these nickel clusters are considered systematically. The ground spin state and the lowest energy isomers are identified for each cluster size. The results are compared to available experimental and other theoretical data. The molecular orbitals of the largest cluster are plotted for all spin states. The relative stabilities of these states are interpreted in terms of superatom orbitals and no-pair bonding.     

A density functional study of chemical,magnetic and thermodynamic properties of small palladium clusters

Structural, chemical, magnetic and thermodynamic properties of palladium clusters Pd_n with n = 2–11 are studied using density functional methods. The average bond length, entropy, enthalpy and polarisability are observed to increase as the cluster grows in size. The binding energy per atom also increases with cluster size. Stability function and atom addition energy change predict that Pd₄, Pd₆ and Pd₉ are relatively more stable than their neighbouring clusters. Electron affinity, electronegativity and electrophilicity values suggest that larger clusters have stronger tendency to accept electrons, thereby supporting the relative stability of Pd₄ and Pd₆. Chemical hardness is also seen to decrease with cluster size, which suggests that large clusters are more prone to changes in their electronic structure. The magnetic properties of these clusters are reported.     

Ab initio investigations on planar (MgO)n clusters (n = 1–5) and their hydrogen adsorption behaviour

Ab initio calculations (B3LYP and PBE-D3) of the structures, stabilities, vibrational, electronic and hydrogen adsorption behaviour of (MgO)_n clusters are performed using 6-311+ + G(d,p) basis set. The planar (MgO)_n clusters are found to be global minima for n ≤ 3 and local minima for n = 4 and 5. In addition, we have also analysed global minimum structures of (MgO)₄ and (MgO)₅. The binding energies suggest that their stabilities increase successively. Vibrational frequencies and IR intensities further support the enhanced stability with an increase in the size of (MgO)_n clusters. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) surfaces are used to explain and discuss the electronic properties. Finally, we have demonstrated hydrogen storage capacity of (MgO)_n clusters, considering hydrogen adsorption on planar as well as global minimum (MgO)₄ and (MgO)₅ clusters. We have noticed that four and five H₂ molecules can be easily adsorbed by (MgO)₄ and (MgO)₅ clusters having adsorption energy of 0.13–0.14 eV with mass ratio of 4.76%. Thus, the present study is expected to motivate further the applications of small clusters for efficient hydrogen energy storage.     

Luminescence and simulation of mixed metal nanoclusters of dicyanoargentate(I) and dicyanoaurate(I) in alkali halides

Heterometallic and homometallic nanoclusters of [Ag(CN)₂]⁻ and [Au(CN)₂]⁻ doped in NaCl, KCl, and NaBr exhibit interesting photophysical phenomenon that are related to the variety of sizes, orientations, and compositions these clusters adopt. Samples of various dopant-host systems have been grown and analyzed with luminescence spectroscopy. In order to predict what types of clusters are in these different systems, an atomistic surface model has been developed that probes the energetics of these clusters as they first form at surface kink sites. An order of preference in mixed-metal systems for heterometallic cluster formation over homometallic cluster formation, NaBr > NaCl > KCl, is predicted which agrees with findings on heterometallic cluster peaks in the luminescence spectra. Structural orientations are predicted to be very different in heterometallic clusters as opposed to homometallic clusters.     

Combinations of Quality and Frequency of Immunization Activities to Stop and Prevent Poliovirus Transmission in the High-Risk Area of Northwest Nigeria

Background

Frequent supplemental immunization activities (SIAs) with the oral poliovirus vaccine (OPV) represent the primary strategy to interrupt poliovirus transmission in the last endemic areas.

Materials and Methods

Using a differential-equation based poliovirus transmission model tailored to high-risk areas in Nigeria, we perform one-way and multi-way sensitivity analyses to demonstrate the impact of different assumptions about routine immunization (RI) and the frequency and quality of SIAs on population immunity to transmission and persistence or emergence of circulating vaccine-derived polioviruses (cVDPVs) after OPV cessation.

Results

More trivalent OPV use remains critical to avoid serotype 2 cVDPVs. RI schedules with or without inactivated polio vaccine (IPV) could significantly improve population immunity if coverage increases well above current levels in under-vaccinated subpopulations. Similarly, the impact of SIAs on overall population immunity and cVDPV risks depends on their ability to reach under-vaccinated groups (i.e., SIA quality). Lower SIA coverage in the under-vaccinated subpopulation results in a higher frequency of SIAs needed to maintain high enough population immunity to avoid cVDPVs after OPV cessation.

Conclusions

National immunization program managers in northwest Nigeria should recognize the benefits of increasing RI and SIA quality. Sufficiently improving RI coverage and improving SIA quality will reduce the frequency of SIAs required to stop and prevent future poliovirus transmission. Better information about the incremental costs to identify and reach under-vaccinated children would help determine the optimal balance between spending to increase SIA and RI quality and spending to increase SIA frequency.     

DFT studies of hydrocarbon combustion on metal surfaces

Catalytic combustion of hydrocarbons is an important technology to produce energy. Compared to conventional flame combustion, the catalyst enables this process to operate at lower temperatures; hence, reducing the energy required for efficient combustion. The reaction and activation energies of direct combustion of hydrocarbons (CH?→?C?+?H) on a series of metal surfaces were investigated using density functional theory (DFT). The data obtained for the Ag, Au, Al, Cu, Rh, Pt, and Pd surfaces were used to investigate the validity of the Brønsted-Evans-Polanyi (BEP) and transition state scaling (TSS) relations for this reaction on these surfaces. These relations were found to be valid (R²?=?0.94 for the BEP correlation and R²?=?1.0 for the TSS correlation) and were therefore used to estimate the energetics of the combustion reaction on Ni, Co, and Fe surfaces. It was found that the estimated transition state and activation energies (E_TS?=??69.70 eV and E_a?=?1.20 eV for Ni, E_TS?=??87.93 eV and E_a?=?1.08 eV for Co and E_TS?=??92.45 eV and E_a?=?0.83 eV for Fe) are in agreement with those obtained by DFT calculations (E_TS?=??69.98 eV and E_a?=?1.23 eV for Ni, E_TS?=??87.88 eV and E_a?=?1.08 eV for Co and E_TS?=??92.57 eV and E_a?=?0.79 eV for Fe). Therefore, these relations can be used to predict energetics of this reaction on these surfaces without doing the time consuming transition state calculations. Also, the calculations show that the activation barrier for CH dissociation decreases in the order Ag ? Au ? Al ? Cu ? Pt ? Pd ? Ni?>?Co?>?Rh?>?Fe.     

Kinetics of reversible N-ethylmaleimide alkylation of metallothionein and the subsequent metal release

 The model alkylating agent N-ethylmaleimide (NEM) reacts reversibly at the metal-bound thiolates of Zn₇MT and Cd₇MT. An unprecedented feature of this reaction is that it approaches equilibrium and requires a large excess of NEM (>1 mM for 3 μM protein) to drive it to completion. The complex kinetics of the reaction can be followed by monitoring the release of bound metal ions using the metallochromic dyes Zincon (ZI) for Zn₇MT and pyridylazoresorcinol for Cd₇MT. An initial lag phase is followed by more rapid release of zinc ions. The observed pseudo-first-order rate constants for the two phases are independent of the ZI and Zn₇MT concentrations. The complex NEM concentration dependence of each phase, k _f, obs=k ^f ₁+k ^f ₂ [NEM] and k _s, obs=k ^s ₁+k ^s ₂ [NEM], demonstrates that the forward reactions are second order and the reverse reactions are first order. The alkylation can be reversed using 2-mercaptoethanol to compete for the protein-bound NEM and regenerate the Zn-binding capability of alkylated MT. An explanation of these observations, based on the reversibility of cysteine alkylation by NEM, was developed and tested. The reactions of Cd₇MT are less complete than those of Zn₇MT and occur more slowly. ¹¹¹Cd-NMR studies of the partially alkylated ¹¹¹Cd₇MT reveal that reaction with only four equivalents of NEM completely alters the cluster structure and eliminates the spectral signatures of the α and β clusters, although very little cadmium has been removed from the protein. This finding substantiates the proposed kinetic intermediate, a partially alkylated MT with complete or nearly complete retention of the metal ions, and rules out the possibility of cooperative reactions at either cluster. Received: 5 August 1996 / Accepted: 24 October 1996     

Theoretical study on the structural,vibrational, and thermodynamic properties of the (Br<Subscript>2</Subscript>GaN<Subscript>3</Subscript>)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–4) clusters

The molecular geometries, vibrational properties, and thermodynamic properties of the clusters (Br₂GaN₃) _n (n = 1–4) were studied at the B3LYP/6-311+G* level. The optimized clusters (Br₂GaN₃) _n (n = 2–4) were all found to possess a cyclic structure consisting of Ga atoms bridged by the α-nitrogen of the azide groups. A discussion of the relationships between the geometrical parameters and the degree of oligomerization n is provided. Features in the IR spectra were assigned by vibrational analysis. Trends in thermodynamic properties with temperature and degree of oligomerization n are discussed. Thermodynamic analysis of the gas-phase reaction showed that the formation of the clusters (Br₂GaN₃) _n (n = 2–4) is thermodynamically favorable considering the enthalpies at 298.2 K. The calculated results for the Gibbs free energies were negative, which indicates that the oligomerizations can occur spontaneously at 298.2 K.     

Numerical taxonomy of psychrotrophic lactic acid bacteria from prepacked meat and meat products

Ninety-four strains of lactic acid bateria isolated from refrigerated, prepacked meat and meat products were together with 59 reference strains of Brochothrix, Lactobacillus, Leuconostoc, Pediococcus and Streptococcus phenotypically classfied, using 96 unit characters. Data were examined using Simple Matching (S_SM) or Jaccard coefficient (S_J), and unweighted pair group algorithm with arithmetic averages. Twenty-three clusters with two or more members were defined at the 84% S_SM-similarity level which corresponded to the S_J-similarity level of 61%. Based on S_SM, most field strains were included in nine clusters, and with three unsignificant exceptions these contained no reference strains. The field clusters were designated Carnobacterium piscicola (cluster 1; 5% of field isolates), Carnobacterium divergens(cluster 2; 9% of field isolates), Leuconostoc (cluster 9; 18% of field isolates) and Lactobacillus (cluster 4, 10, 11, 12, 13 and 14; together 60% of field isolates). The Lactobacillus clusters had many features in common with cluster II of Shaw & Harding (1984). Phenotypical characteristics of major clusters are given. The S_SM and S_J based classifications basically coincided for the field strains; the exception was cluster 4 which now were split in two parts. Fourteen clusters were made up of mainly reference strains (S_SM). Most of them included more than one type strain on species level; exceptions were Brochothrix thermosphacta (cluster 3), Lactobacillus salivarius (cluster 17) and Leuconostoc mesenteroides (cluster 18). Several rearrangements were seen amongst the clusters of the reference strains when S_J, instead of S_SM, was used for clustering.     

Theoretical study on small clusters of BaTiO3 using DFT calculations

Using density functional theory with the generalised gradient approximation, the structural and electronic properties of small (BaTiO₃)_n (n = 1–4) clusters have been studied. All the analysed growth modes were observed to consist of the same unit block, which in turn is similar to the well-known (TiO₂)₂ cluster. The BaTiO₃ and (BaTiO₃)₂ systems were observed to adopt analogous geometries to the ground state of (TiO₂)_n clusters with C_s and D_2h symmetries, respectively. The calculated value of the energy gap for the studied (BaTiO₃)_n clusters tends to approach that observed for its tetragonal bulk BaTiO₃ counterpart when n ≥ 3 is considered; the same tendency is observed for the Ba–Ba, Ba–Ti, Ti–O and Ba–Ti interatomic distances. For all the (BaTiO₃)_n clusters, the structural characteristics of their respective isomers were explored.     

Structures and excitation energies of ozone-water clusters O3(H2O)n (n = 1-4)

Hybrid density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations have been carried out for ozone-water clusters O₃(H₂O)_n (n = 1-4) in order to obtain hydration effects on the absorption spectrum of ozone. The first water molecule in n = 1 is bound to the ozone molecule by an oxygen orientation form in which the oxygen atom of H₂O orients the central oxygen atom of O₃. In n = 2, the water dimer is bound to O₃ and then the cyclic structure is formed as the most stable structure. For n = 3 (or n = 4), the cyclic water trimer (or tetramer) is bound by a hydrogen bond to the ozone molecule. The TD-DFT calculations of O₃(H₂O)_n (n = 0-4) show that the first and second excitation energies of O₃ are blue-shifted by the interaction with the water clusters. The magnitude of the spectral shift is largest in n = 2, and the shifts of the excitation energies are +0.07 eV for S₁ and +0.13 eV for S₂ states. In addition to the spectral shifts (S₁ and S₂ states), it is suggested that a charge-transfer band is appeared as a low-lying excited state above the S₁ and S₂ states. The origin of the spectrum shifts was discussed on the basis of theoretical results.     

Molecular dynamics study of the initial stages of catalyzed single-wall carbon nanotubes growth: force field development

Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes are modified to simulate the catalyzed growth of single-wall carbon nanotubes on Ni_n clusters with n >20, and the reactive empirical bond order Brenner potential for C-C interactions is also revised to include the effect of the metal atoms on such interactions. Figure Force field parameters for carbon-metal interactions obtained from DFT calculations in small clusters.     

Structures and stabilities of ScBn (n = 1–12) clusters: an ab initio investigation

The geometries, stabilities, and electronic properties of ScB_n (n?=?1–12) clusters have been systematically investigated by using density functional theory B3LYP method and coupled–cluster theory CCSD(T) method. It is found that the ground state isomers of ScB_n have planar or quasi–planar structure when n?≤?6, which can be viewed as a B atom of the corresponding B_n+1 cluster is substituted by a Sc atom. From n?≥?7, the ground state isomers favor nest–like structure, in which the Sc atom sits on a nest–like B_n cluster. The calculated second–order differences of energies manifest that the magic numbers of stability are n?=?3, 7, 8, 9 and 11 for the ScB _n clusters. Further analysis indicates that the ScB₇ cluster with C _6v symmetry represents the outstanding stable ScB_n cluster, as confirmed by its electronic structure and molecular orbitals.     

A DFT study on equilibrium geometries, stabilities, and electronic properties of small bimetallic Na-doped Au(n) (n = 1-9) clusters: comparison with pure gold clusters

A systematic study on the geometric structures, relative stabilities, and electronic properties of small bimetallic Au _n Na (n = 1-9) clusters has been performed by means of first-principle density functional theory calculations at the PW91PW91 level. The results show that the optimized ground-state isomers adopt planar structures up to n = 5, and the Na-capped geometries are dominant growth patterns for n = 6-9. Dramatic odd-even alternative behaviors are obtained in the second-order difference of energies, fragmentation energies, highest occupied-lowest unoccupied molecular orbital energy gaps, and chemical hardness for both Au _n Na and Au _n+1 clusters. It is found that Au₅Na and Au₆ have the most enhanced stability. Here, the size evolutions of the theoretical ionization potentials are in agreement with available experimental data, suggesting a good prediction of the lowest energy structures in the present study. In addition, the charge transfer has been analyzed on the basis of natural population analysis.